Reformat RNA FASTA to DNA FASTA for reference

reformat_rna_ref.sh

#!/bin/bash
#
# Get miRBase hairpin FASTA (multiline, with U instead of T) and reformat it to "normal" reference FASTA
#

wget ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz # Get the sequence

zcat hairpin.fa.gz | perl -pe '/^>/ ? print "\n" : chomp' \
    | tail -n +2 | sed '/^[^>]/ y/uU/tT/' \
    > hairpin.oneline.fasta # Convert to one-line fasta and replace all Us for Ts
    
grep -A1 "^>hsa" hairpin.oneline.fasta | sed '/^--$/d' \
    > hsa_hairpin.fasta # Get only human hairpin sequences